FAQ for Halo 4: The Rise Of The Covenant.

Will Master Chief appear in this movie?
No. This film is before Master Chief's time. He won't appear in the movie. Master Chief's actor also said he won't be interested now into playing the character.

Is it true that Halo 4: The Rise Of The Covenant is the beginning of a prequel trilogy?
Yes. Bungie officialy confirmed that Halo 4, 5 and 6 will completely focus entirely on the beginning of the war.

Will this movie be in 3D?
Bungie is still considering if the movie will be released in 3D. Bungie said that the movie will be in IMAX.

If Halo 4 is coming, will Marathon 4 also be released?
Bungie said that Marathon 3 is actually the last film in the series. Also after Halo 4, he will begin working on Suldrun's Garden, this will be a film adaption to a fantasy-book.

Will the Flood appear?
Possibly. Not revealed. It is isn't known how the Flood was related to the beginning of the war.

So the question is currently unknown.